Hi ALL,
I have a protein pdb file generated using MODELLER. When I use the pdb2gmx
command on it, it throws the error:
Atom -C not found in residue MET1 while adding hydrogens
and
Atom OXT in residue LEU 404
The initial and end of the pdb file is like this:
---------------------------------------------------------------------------------
CRYST1 116.083 116.083 116.083 90.00 90.00 90.00 P 1 1
ATOM 1 N MET X 1 67.960 51.279 76.751 1.00 0.00
ATOM 2 CA MET X 1 67.510 49.899 76.451 1.00 0.00
ATOM 3 CB MET X 1 65.990 49.769 76.661 1.00 0.00
ATOM 4 CG MET X 1 65.570 49.959 78.111 1.00 0.00
ATOM 5 SD MET X 1 63.780 49.819 78.401 1.00 0.00
ATOM 6 CE MET X 1 63.370 51.379 77.561 1.00 0.00
ATOM 7 C MET X 1 67.840 49.539 75.041 1.00 0.00
ATOM 8 O MET X 1 68.870 49.949 74.511 1.00 0.00
ATOM 9 N ALA X 2 66.970 48.749 74.401 1.00 0.00
ATOM 10 CA ALA X 2 67.240 48.349 73.051 1.00 0.00
ATOM 11 CB ALA X 2 66.160 47.429 72.461 1.00 0.00
ATOM 12 C ALA X 2 67.290 49.579 72.221 1.00 0.00
.
.
.
ATOM 3069 OD2 ASP X 403 43.890 88.349 36.411 1.00 0.00
ATOM 3070 C ASP X 403 42.590 84.299 34.251 1.00 0.00
ATOM 3071 O ASP X 403 41.820 84.059 33.321 1.00 0.00
ATOM 3072 N LEU X 404 42.790 83.449 35.281 1.00 0.00
ATOM 3073 CA LEU X 404 42.100 82.199 35.401 1.00 0.00
ATOM 3074 CB LEU X 404 42.250 81.559 36.791 1.00 0.00
ATOM 3075 CG LEU X 404 43.710 81.209 37.151 1.00 0.00
ATOM 3076 CD1 LEU X 404 44.580 82.469 37.241 1.00 0.00
ATOM 3077 CD2 LEU X 404 43.770 80.349 38.431 1.00 0.00
ATOM 3078 C LEU X 404 40.610 82.469 35.201 1.00 0.00
ATOM 3079 O LEU X 404 40.010 81.799 34.311 1.00 0.00
ATOM 3080 OXT LEU X 404 40.050 83.329 35.931 1.00 0.00
END
--------------------------------------------------------------------------------------
How can I remove these errors? Do I need to modify the pdb file anyway?
Any suggestion is welcome.
Regards,
Anirban GhoshGrade Based Engineer
Bioinformatics Team
Centre for Development of Advanced Computing (C-DAC)
Pune, India
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